Variant report

Variant	rs1216802
Chromosome Location	chr1:113636924-113636925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113634658..113637321-chr1:113637613..113639696,2	MCF-7	breast:
2	chr1:113614838..113617488-chr1:113635927..113637918,2	MCF-7	breast:
3	chr1:113635215..113637983-chr1:114201241..114204129,2	K562	blood:
4	chr1:113629031..113632122-chr1:113632833..113640329,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238198	Chromatin interaction
ENSG00000198799	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11102584	1.00[ASN][1000 genomes]
rs11102586	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102588	1.00[ASN][1000 genomes]
rs11102592	1.00[ASN][1000 genomes]
rs12071491	1.00[EUR][1000 genomes]
rs12117273	0.86[EUR][1000 genomes]
rs12118532	0.86[EUR][1000 genomes]
rs12120738	0.86[EUR][1000 genomes]
rs12123072	0.86[EUR][1000 genomes]
rs12123519	0.86[EUR][1000 genomes]
rs12123601	0.86[EUR][1000 genomes]
rs12128658	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133057	0.86[EUR][1000 genomes]
rs12136941	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137299	0.86[EUR][1000 genomes]
rs12140067	1.00[EUR][1000 genomes]
rs12141415	0.86[EUR][1000 genomes]
rs12143171	0.86[EUR][1000 genomes]
rs12143341	0.86[EUR][1000 genomes]
rs1216767	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216769	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216793	1.00[ASN][1000 genomes]
rs1216798	1.00[ASN][1000 genomes]
rs1216805	1.00[ASN][1000 genomes]
rs1216807	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216808	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216810	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1216812	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1216813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12184272	0.86[EUR][1000 genomes]
rs12184320	0.86[EUR][1000 genomes]
rs12744661	0.86[EUR][1000 genomes]
rs1310142	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618794	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17031006	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1728227	1.00[ASN][1000 genomes]
rs1728229	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1728240	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1766864	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778016	1.00[ASN][1000 genomes]
rs1778017	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778023	0.83[ASN][1000 genomes]
rs41296184	1.00[ASN][1000 genomes]
rs4839291	1.00[ASN][1000 genomes]
rs4839292	1.00[ASN][1000 genomes]
rs6670587	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6695183	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74111210	1.00[ASN][1000 genomes]
rs74111213	1.00[ASN][1000 genomes]
rs7531847	1.00[ASN][1000 genomes]
rs7545814	1.00[EUR][1000 genomes]
rs946215	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
7	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
11	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv437002	chr1:113592588-113658887	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113616800-113638600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:113617000-113638400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:113617000-113645800	Weak transcription	Aorta	Aorta
4	chr1:113617200-113642600	Weak transcription	A549	lung
5	chr1:113617400-113638000	Weak transcription	NHLF	lung
6	chr1:113617800-113637200	Weak transcription	Psoas Muscle	Psoas
7	chr1:113617800-113637800	Weak transcription	Spleen	Spleen
8	chr1:113617800-113638000	Weak transcription	Gastric	stomach
9	chr1:113622000-113637200	Weak transcription	Colonic Mucosa	Colon
10	chr1:113622000-113637800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:113622000-113638400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:113622000-113638400	Weak transcription	Brain Germinal Matrix	brain
13	chr1:113622200-113645600	Weak transcription	Right Ventricle	heart
14	chr1:113622200-113645800	Weak transcription	Lung	lung
15	chr1:113624000-113638400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:113624400-113637800	Weak transcription	Pancreas	Pancrea
17	chr1:113625200-113637200	Weak transcription	Thymus	Thymus
18	chr1:113625200-113638200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:113625800-113646000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:113626400-113637200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:113626400-113638200	Weak transcription	Esophagus	oesophagus
22	chr1:113628200-113637200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:113629800-113637800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:113630800-113638600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:113631000-113638400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:113631600-113638000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:113631800-113638800	Weak transcription	Fetal Brain Female	brain
28	chr1:113631800-113666600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:113632000-113637200	Weak transcription	Brain Anterior Caudate	brain
30	chr1:113632000-113638000	Weak transcription	Ovary	ovary
31	chr1:113632000-113638400	Weak transcription	Brain Angular Gyrus	brain
32	chr1:113632000-113638400	Weak transcription	Brain Substantia Nigra	brain
33	chr1:113632400-113637000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:113633200-113638000	Weak transcription	Fetal Heart	heart
35	chr1:113633600-113672600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:113633800-113670000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr1:113633800-113672600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:113634200-113655200	Strong transcription	Hela-S3	cervix
39	chr1:113634200-113656000	Strong transcription	Dnd41	blood
40	chr1:113634200-113669800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:113634200-113669800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:113634200-113670000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:113634200-113671400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:113634200-113673000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:113634400-113639800	Strong transcription	GM12878-XiMat	blood
46	chr1:113634400-113655600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:113634400-113672600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:113634600-113644800	Strong transcription	Placenta	Placenta
49	chr1:113634600-113646800	Strong transcription	Primary hematopoietic stem cells	blood
50	chr1:113634600-113652200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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